Basics of membrane-protein interactions using molecular dynamics with NAMD, VMD, and CHARMM-GUI

This tutorial is designed to introduce the preparation, modeling, and analysis of membrane-protein system with molecular dynamics (MD) using NAMD, VMD, and CHARMM-GUI.  The system of interest will be the outer membrane phospholipase A from E. coli (OmpLA, PDB ID 1QD5, Snijder HJ, …,  Dijkstra BW, Nature, 401, 717, 1999). In a recent experimental study the Fleming Lab (Johns Hopkins) used spontaneous folding of OmpLA into the membrane to prepare a hydrophobicity scale (Moon PC and Fleming KG, PNAS 108, 10174, 2011)

 

Estimated time to complete this tutorial is 1.5 hr.

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charmm-gui-ompla-tutorial-ver-1.1-17-Aug-2016-smaller.pdf1.59 MB